Starting phenix.real_space_refine on Sun Apr 14 10:44:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j04_35883/04_2024/8j04_35883_neut_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 88 5.16 5 C 10068 2.51 5 N 2616 2.21 5 O 2800 1.98 5 F 8 1.80 5 H 15244 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "H PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30824 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5478 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 6, 'TRANS': 325} Chain breaks: 2 Chain: "B" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5478 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 6, 'TRANS': 325} Chain breaks: 2 Chain: "C" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5478 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 6, 'TRANS': 325} Chain breaks: 2 Chain: "E" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 5478 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 6, 'TRANS': 325} Chain breaks: 2 Chain: "H" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2178 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.83, per 1000 atoms: 0.45 Number of scatterers: 30824 At special positions: 0 Unit cell: (121.83, 121.83, 106.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 F 8 9.00 O 2800 8.00 N 2616 7.00 C 10068 6.00 H 15244 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.68 Conformation dependent library (CDL) restraints added in 3.0 seconds 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 91 through 113 Processing helix chain 'A' and resid 119 through 150 removed outlier: 3.897A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N CYS A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.789A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 254 Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 329 removed outlier: 3.790A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 536 through 557 Processing helix chain 'A' and resid 564 through 577 Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 113 Processing helix chain 'B' and resid 119 through 150 removed outlier: 3.899A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N CYS B 150 " --> pdb=" O TRP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.787A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 254 Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 329 removed outlier: 3.784A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 358 through 365 Processing helix chain 'B' and resid 536 through 557 Processing helix chain 'B' and resid 564 through 577 Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 83 through 93 Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 91 through 113 Processing helix chain 'D' and resid 119 through 150 removed outlier: 3.896A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.786A pdb=" N MET D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 229 through 254 Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 329 removed outlier: 3.781A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 333 through 349 Processing helix chain 'D' and resid 358 through 365 Processing helix chain 'D' and resid 536 through 557 Processing helix chain 'D' and resid 564 through 577 Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 103 through 110 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'F' and resid 103 through 112 removed outlier: 3.653A pdb=" N THR F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN F 112 " --> pdb=" O HIS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 91 through 113 Processing helix chain 'G' and resid 119 through 150 removed outlier: 3.910A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N CYS G 150 " --> pdb=" O TRP G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 154 No H-bonds generated for 'chain 'G' and resid 152 through 154' Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'G' and resid 197 through 211 removed outlier: 3.786A pdb=" N MET G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 229 through 254 Processing helix chain 'G' and resid 264 through 275 Processing helix chain 'G' and resid 288 through 329 removed outlier: 3.789A pdb=" N LEU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix Processing helix chain 'G' and resid 333 through 349 Processing helix chain 'G' and resid 358 through 365 Processing helix chain 'G' and resid 536 through 557 Processing helix chain 'G' and resid 564 through 577 Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 83 through 93 Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 139 through 145 996 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.56 Time building geometry restraints manager: 28.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15216 1.03 - 1.23: 52 1.23 - 1.42: 6920 1.42 - 1.62: 8828 1.62 - 1.81: 148 Bond restraints: 31164 Sorted by residual: bond pdb=" C ARG D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.329 1.340 -0.010 1.22e-02 6.72e+03 6.78e-01 bond pdb=" CB LYS C 76 " pdb=" CG LYS C 76 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.68e-01 bond pdb=" CB LYS E 76 " pdb=" CG LYS E 76 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.41e-01 bond pdb=" C ALA G 294 " pdb=" O ALA G 294 " ideal model delta sigma weight residual 1.237 1.227 0.009 1.17e-02 7.31e+03 6.40e-01 bond pdb=" CB LYS F 76 " pdb=" CG LYS F 76 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.40e-01 ... (remaining 31159 not shown) Histogram of bond angle deviations from ideal: 97.32 - 113.80: 35906 113.80 - 130.28: 19976 130.28 - 146.76: 74 146.76 - 163.23: 0 163.23 - 179.71: 8 Bond angle restraints: 55964 Sorted by residual: angle pdb=" CA MET F 125 " pdb=" CB MET F 125 " pdb=" CG MET F 125 " ideal model delta sigma weight residual 114.10 119.20 -5.10 2.00e+00 2.50e-01 6.51e+00 angle pdb=" CA MET H 125 " pdb=" CB MET H 125 " pdb=" CG MET H 125 " ideal model delta sigma weight residual 114.10 119.18 -5.08 2.00e+00 2.50e-01 6.44e+00 angle pdb=" CA MET C 125 " pdb=" CB MET C 125 " pdb=" CG MET C 125 " ideal model delta sigma weight residual 114.10 119.17 -5.07 2.00e+00 2.50e-01 6.42e+00 angle pdb=" CA MET E 125 " pdb=" CB MET E 125 " pdb=" CG MET E 125 " ideal model delta sigma weight residual 114.10 119.09 -4.99 2.00e+00 2.50e-01 6.23e+00 angle pdb=" CA PRO D 88 " pdb=" C PRO D 88 " pdb=" N ARG D 89 " ideal model delta sigma weight residual 114.58 117.35 -2.77 1.16e+00 7.43e-01 5.71e+00 ... (remaining 55959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 12632 17.41 - 34.83: 1220 34.83 - 52.24: 472 52.24 - 69.66: 128 69.66 - 87.07: 24 Dihedral angle restraints: 14476 sinusoidal: 7700 harmonic: 6776 Sorted by residual: dihedral pdb=" CA ASP H 81 " pdb=" CB ASP H 81 " pdb=" CG ASP H 81 " pdb=" OD1 ASP H 81 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP F 81 " pdb=" CB ASP F 81 " pdb=" CG ASP F 81 " pdb=" OD1 ASP F 81 " ideal model delta sinusoidal sigma weight residual -30.00 -89.10 59.10 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP E 81 " pdb=" CB ASP E 81 " pdb=" CG ASP E 81 " pdb=" OD1 ASP E 81 " ideal model delta sinusoidal sigma weight residual -30.00 -89.06 59.06 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 14473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1486 0.025 - 0.050: 522 0.050 - 0.075: 224 0.075 - 0.100: 59 0.100 - 0.125: 25 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CA ILE F 64 " pdb=" N ILE F 64 " pdb=" C ILE F 64 " pdb=" CB ILE F 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE H 64 " pdb=" N ILE H 64 " pdb=" C ILE H 64 " pdb=" CB ILE H 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 2313 not shown) Planarity restraints: 4560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C04 9MF A 801 " 0.010 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C15 9MF A 801 " 0.010 2.00e-02 2.50e+03 pdb=" C18 9MF A 801 " 0.010 2.00e-02 2.50e+03 pdb=" N14 9MF A 801 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 9MF G 802 " 0.010 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C15 9MF G 802 " 0.010 2.00e-02 2.50e+03 pdb=" C18 9MF G 802 " 0.010 2.00e-02 2.50e+03 pdb=" N14 9MF G 802 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C04 9MF B 802 " 0.009 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C15 9MF B 802 " 0.009 2.00e-02 2.50e+03 pdb=" C18 9MF B 802 " 0.009 2.00e-02 2.50e+03 pdb=" N14 9MF B 802 " -0.028 2.00e-02 2.50e+03 ... (remaining 4557 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2461 2.21 - 2.81: 65063 2.81 - 3.40: 88171 3.40 - 4.00: 111006 4.00 - 4.60: 171444 Nonbonded interactions: 438145 Sorted by model distance: nonbonded pdb=" O VAL F 143 " pdb=" HG1 THR F 147 " model vdw 1.609 1.850 nonbonded pdb=" O VAL C 143 " pdb=" HG1 THR C 147 " model vdw 1.609 1.850 nonbonded pdb=" O VAL E 143 " pdb=" HG1 THR E 147 " model vdw 1.610 1.850 nonbonded pdb=" O VAL H 143 " pdb=" HG1 THR H 147 " model vdw 1.611 1.850 nonbonded pdb=" O PHE E 90 " pdb=" H ASP E 94 " model vdw 1.634 1.850 ... (remaining 438140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.480 Extract box with map and model: 4.940 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 98.680 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15920 Z= 0.206 Angle : 0.510 6.572 21480 Z= 0.271 Chirality : 0.033 0.125 2316 Planarity : 0.003 0.040 2708 Dihedral : 17.202 87.069 5736 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.93 % Allowed : 24.26 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.20), residues: 1868 helix: 1.93 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : 0.01 (0.38), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 288 HIS 0.001 0.000 HIS B 328 PHE 0.012 0.001 PHE G 304 TYR 0.011 0.001 TYR D 571 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.3126 (ptm-80) cc_final: 0.1659 (tpm170) REVERT: A 152 CYS cc_start: 0.6194 (m) cc_final: 0.5794 (t) REVERT: A 198 ARG cc_start: 0.4769 (mtt180) cc_final: 0.4435 (tpt-90) REVERT: A 298 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8685 (m) REVERT: A 327 LYS cc_start: 0.8014 (tmmm) cc_final: 0.7808 (tttt) REVERT: B 116 LYS cc_start: 0.8937 (tppp) cc_final: 0.8733 (mmtm) REVERT: B 161 LEU cc_start: 0.8048 (tt) cc_final: 0.7724 (tm) REVERT: B 289 ASN cc_start: 0.8064 (m-40) cc_final: 0.7714 (m-40) REVERT: B 298 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8857 (m) REVERT: B 578 MET cc_start: 0.2671 (ttt) cc_final: 0.2469 (ttt) REVERT: C 110 MET cc_start: 0.3829 (tpp) cc_final: 0.2776 (mmp) REVERT: D 80 PHE cc_start: 0.8343 (t80) cc_final: 0.8060 (t80) REVERT: D 130 GLU cc_start: 0.7716 (tt0) cc_final: 0.7430 (tt0) REVERT: E 110 MET cc_start: 0.4048 (tpp) cc_final: 0.2846 (mmp) REVERT: F 76 LYS cc_start: -0.1698 (OUTLIER) cc_final: -0.2514 (tttm) REVERT: F 110 MET cc_start: 0.3968 (tpp) cc_final: 0.2558 (mmp) REVERT: G 198 ARG cc_start: 0.5272 (mtt180) cc_final: 0.4979 (tpt-90) REVERT: G 298 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8598 (m) REVERT: G 344 TRP cc_start: 0.4236 (t-100) cc_final: 0.3947 (t-100) REVERT: H 110 MET cc_start: 0.4008 (tpp) cc_final: 0.2393 (mmp) outliers start: 15 outliers final: 3 residues processed: 193 average time/residue: 2.7770 time to fit residues: 594.1172 Evaluate side-chains 167 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 298 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15920 Z= 0.301 Angle : 0.523 5.740 21480 Z= 0.276 Chirality : 0.035 0.130 2316 Planarity : 0.004 0.072 2708 Dihedral : 6.498 69.136 2147 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.04 % Allowed : 23.89 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1868 helix: 1.76 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.04 (0.38), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 344 HIS 0.003 0.001 HIS B 96 PHE 0.017 0.001 PHE A 163 TYR 0.017 0.001 TYR A 237 ARG 0.010 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6213 (m) cc_final: 0.5846 (t) REVERT: A 198 ARG cc_start: 0.4792 (mtt180) cc_final: 0.4448 (tpt-90) REVERT: A 322 GLU cc_start: 0.7338 (pp20) cc_final: 0.7109 (pp20) REVERT: B 161 LEU cc_start: 0.8227 (tt) cc_final: 0.7801 (tm) REVERT: B 177 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8186 (pp) REVERT: B 214 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8035 (mtp85) REVERT: C 110 MET cc_start: 0.3851 (tpp) cc_final: 0.2721 (mmp) REVERT: D 80 PHE cc_start: 0.8495 (t80) cc_final: 0.8250 (t80) REVERT: D 578 MET cc_start: 0.2908 (ttt) cc_final: 0.2583 (ttt) REVERT: E 110 MET cc_start: 0.4409 (tpp) cc_final: 0.3222 (mmp) REVERT: E 141 GLU cc_start: 0.3707 (OUTLIER) cc_final: 0.3049 (pp20) REVERT: F 110 MET cc_start: 0.4095 (tpp) cc_final: 0.2617 (mmp) REVERT: G 198 ARG cc_start: 0.5338 (mtt180) cc_final: 0.5047 (tpt-90) REVERT: G 289 ASN cc_start: 0.8335 (m-40) cc_final: 0.8095 (m110) REVERT: G 344 TRP cc_start: 0.4218 (t-100) cc_final: 0.3946 (t-100) REVERT: H 110 MET cc_start: 0.4425 (tpp) cc_final: 0.2796 (mmp) outliers start: 33 outliers final: 12 residues processed: 187 average time/residue: 2.3430 time to fit residues: 494.4066 Evaluate side-chains 169 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain H residue 77 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15920 Z= 0.410 Angle : 0.547 8.361 21480 Z= 0.290 Chirality : 0.036 0.143 2316 Planarity : 0.004 0.052 2708 Dihedral : 6.550 81.522 2134 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.23 % Allowed : 24.50 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 1868 helix: 1.72 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.03 (0.37), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 344 HIS 0.003 0.001 HIS B 96 PHE 0.021 0.001 PHE A 163 TYR 0.012 0.001 TYR A 237 ARG 0.002 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5599 (t) REVERT: A 198 ARG cc_start: 0.4969 (mtt180) cc_final: 0.4632 (tpt-90) REVERT: A 322 GLU cc_start: 0.7466 (pp20) cc_final: 0.7251 (pp20) REVERT: B 152 CYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6336 (t) REVERT: B 214 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8083 (mtp85) REVERT: B 289 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.7808 (m-40) REVERT: B 578 MET cc_start: 0.2769 (ttt) cc_final: 0.2532 (ttt) REVERT: C 110 MET cc_start: 0.3876 (tpp) cc_final: 0.2723 (mmp) REVERT: D 80 PHE cc_start: 0.8495 (t80) cc_final: 0.8277 (t80) REVERT: D 578 MET cc_start: 0.3097 (ttt) cc_final: 0.2877 (ttt) REVERT: E 110 MET cc_start: 0.4504 (tpp) cc_final: 0.3205 (mmp) REVERT: E 141 GLU cc_start: 0.3762 (OUTLIER) cc_final: 0.3096 (pp20) REVERT: F 110 MET cc_start: 0.3968 (tpp) cc_final: 0.2486 (mmp) REVERT: G 198 ARG cc_start: 0.5322 (mtt180) cc_final: 0.5117 (tpt-90) REVERT: G 289 ASN cc_start: 0.8464 (m-40) cc_final: 0.8168 (m110) REVERT: G 344 TRP cc_start: 0.4148 (t-100) cc_final: 0.3925 (t-100) REVERT: H 110 MET cc_start: 0.4477 (tpp) cc_final: 0.2926 (mmp) REVERT: H 141 GLU cc_start: 0.4082 (OUTLIER) cc_final: 0.3337 (pp20) outliers start: 36 outliers final: 16 residues processed: 184 average time/residue: 2.5316 time to fit residues: 522.6231 Evaluate side-chains 177 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 152 CYS Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 141 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.0870 chunk 128 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 50.0000 chunk 171 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15920 Z= 0.154 Angle : 0.468 5.979 21480 Z= 0.250 Chirality : 0.032 0.125 2316 Planarity : 0.003 0.042 2708 Dihedral : 6.115 61.531 2132 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.11 % Allowed : 25.62 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 1868 helix: 1.85 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : 0.04 (0.38), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.001 0.000 HIS D 575 PHE 0.009 0.001 PHE B 304 TYR 0.010 0.001 TYR B 571 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6308 (m) cc_final: 0.5702 (t) REVERT: A 198 ARG cc_start: 0.4908 (mtt180) cc_final: 0.4564 (tpt-90) REVERT: A 322 GLU cc_start: 0.7483 (pp20) cc_final: 0.7214 (pp20) REVERT: B 161 LEU cc_start: 0.8228 (tt) cc_final: 0.7890 (tm) REVERT: B 214 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8042 (mtp85) REVERT: B 578 MET cc_start: 0.2779 (ttt) cc_final: 0.2522 (ttt) REVERT: C 110 MET cc_start: 0.3878 (tpp) cc_final: 0.2801 (mmp) REVERT: D 80 PHE cc_start: 0.8474 (t80) cc_final: 0.8240 (t80) REVERT: E 110 MET cc_start: 0.4471 (tpp) cc_final: 0.3240 (mmp) REVERT: F 110 MET cc_start: 0.3980 (tpp) cc_final: 0.2494 (mmp) REVERT: G 198 ARG cc_start: 0.5302 (mtt180) cc_final: 0.5043 (tpt-90) REVERT: G 289 ASN cc_start: 0.8399 (m-40) cc_final: 0.7724 (m-40) REVERT: G 344 TRP cc_start: 0.4065 (t-100) cc_final: 0.3839 (t-100) REVERT: H 110 MET cc_start: 0.4406 (tpp) cc_final: 0.2957 (mmp) outliers start: 18 outliers final: 11 residues processed: 173 average time/residue: 2.4516 time to fit residues: 484.7030 Evaluate side-chains 164 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain H residue 77 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 163 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15920 Z= 0.282 Angle : 0.501 6.295 21480 Z= 0.265 Chirality : 0.034 0.128 2316 Planarity : 0.004 0.047 2708 Dihedral : 6.206 62.743 2132 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.92 % Allowed : 25.50 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1868 helix: 1.85 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -0.05 (0.37), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 344 HIS 0.003 0.000 HIS A 357 PHE 0.016 0.001 PHE B 304 TYR 0.011 0.001 TYR B 571 ARG 0.002 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6235 (m) cc_final: 0.5730 (t) REVERT: A 198 ARG cc_start: 0.4935 (mtt180) cc_final: 0.4611 (tpt-90) REVERT: A 322 GLU cc_start: 0.7483 (pp20) cc_final: 0.7268 (pp20) REVERT: A 360 TRP cc_start: 0.0900 (m-10) cc_final: 0.0678 (m-10) REVERT: B 161 LEU cc_start: 0.8263 (tt) cc_final: 0.7924 (tm) REVERT: B 214 ARG cc_start: 0.8603 (tpp80) cc_final: 0.7949 (mtp85) REVERT: B 578 MET cc_start: 0.2922 (ttt) cc_final: 0.2651 (ttt) REVERT: C 110 MET cc_start: 0.3963 (tpp) cc_final: 0.2945 (mmp) REVERT: D 80 PHE cc_start: 0.8482 (t80) cc_final: 0.8278 (t80) REVERT: D 214 ARG cc_start: 0.8417 (tpp80) cc_final: 0.7817 (mtt90) REVERT: E 110 MET cc_start: 0.4356 (tpp) cc_final: 0.3145 (mmp) REVERT: F 110 MET cc_start: 0.4037 (tpp) cc_final: 0.2554 (mmp) REVERT: F 125 MET cc_start: 0.0784 (mpt) cc_final: 0.0267 (mpt) REVERT: G 198 ARG cc_start: 0.5359 (mtt180) cc_final: 0.5074 (tpt-90) REVERT: G 289 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7877 (m-40) REVERT: G 344 TRP cc_start: 0.4028 (t-100) cc_final: 0.3816 (t-100) REVERT: H 110 MET cc_start: 0.4366 (tpp) cc_final: 0.2846 (mmp) outliers start: 31 outliers final: 16 residues processed: 185 average time/residue: 2.5067 time to fit residues: 520.0367 Evaluate side-chains 175 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 77 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 30.0000 chunk 163 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15920 Z= 0.243 Angle : 0.491 6.495 21480 Z= 0.260 Chirality : 0.034 0.145 2316 Planarity : 0.004 0.046 2708 Dihedral : 6.112 60.530 2132 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.49 % Allowed : 25.62 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1868 helix: 1.85 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -0.05 (0.37), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 344 HIS 0.002 0.000 HIS D 575 PHE 0.018 0.001 PHE B 163 TYR 0.011 0.001 TYR B 571 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6218 (m) cc_final: 0.5672 (t) REVERT: A 198 ARG cc_start: 0.4885 (mtt180) cc_final: 0.4630 (tpt-90) REVERT: A 322 GLU cc_start: 0.7488 (pp20) cc_final: 0.7212 (pp20) REVERT: B 161 LEU cc_start: 0.8247 (tt) cc_final: 0.7905 (tm) REVERT: B 214 ARG cc_start: 0.8605 (tpp80) cc_final: 0.7956 (mtp85) REVERT: B 578 MET cc_start: 0.2948 (ttt) cc_final: 0.2671 (ttt) REVERT: C 110 MET cc_start: 0.3957 (tpp) cc_final: 0.2884 (mmp) REVERT: D 80 PHE cc_start: 0.8470 (t80) cc_final: 0.8265 (t80) REVERT: D 214 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7827 (mtt90) REVERT: E 110 MET cc_start: 0.4345 (tpp) cc_final: 0.3185 (mmp) REVERT: F 110 MET cc_start: 0.4031 (tpp) cc_final: 0.2579 (mmp) REVERT: G 198 ARG cc_start: 0.5342 (mtt180) cc_final: 0.5029 (tpt-90) REVERT: G 289 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7872 (m-40) REVERT: H 110 MET cc_start: 0.4363 (tpp) cc_final: 0.2866 (mmp) outliers start: 24 outliers final: 16 residues processed: 178 average time/residue: 2.4511 time to fit residues: 490.6097 Evaluate side-chains 170 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 50.0000 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 181 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15920 Z= 0.187 Angle : 0.480 6.708 21480 Z= 0.254 Chirality : 0.033 0.129 2316 Planarity : 0.003 0.045 2708 Dihedral : 6.025 60.941 2132 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.30 % Allowed : 25.74 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.20), residues: 1868 helix: 1.88 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -0.04 (0.37), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 344 HIS 0.006 0.000 HIS A 357 PHE 0.014 0.001 PHE B 163 TYR 0.011 0.001 TYR B 571 ARG 0.001 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6188 (m) cc_final: 0.5657 (t) REVERT: A 198 ARG cc_start: 0.4859 (mtt180) cc_final: 0.4615 (tpt-90) REVERT: A 322 GLU cc_start: 0.7454 (pp20) cc_final: 0.7199 (pp20) REVERT: B 161 LEU cc_start: 0.8240 (tt) cc_final: 0.7894 (tm) REVERT: B 214 ARG cc_start: 0.8598 (tpp80) cc_final: 0.7956 (mtp85) REVERT: B 578 MET cc_start: 0.2949 (ttt) cc_final: 0.2675 (ttt) REVERT: C 110 MET cc_start: 0.3989 (tpp) cc_final: 0.2934 (mmp) REVERT: D 80 PHE cc_start: 0.8461 (t80) cc_final: 0.8259 (t80) REVERT: D 214 ARG cc_start: 0.8411 (tpp80) cc_final: 0.7838 (mtt90) REVERT: E 110 MET cc_start: 0.4338 (tpp) cc_final: 0.3192 (mmp) REVERT: F 110 MET cc_start: 0.4041 (tpp) cc_final: 0.2595 (mmp) REVERT: G 198 ARG cc_start: 0.5304 (mtt180) cc_final: 0.5010 (tpt-90) REVERT: G 289 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7785 (m-40) REVERT: H 110 MET cc_start: 0.4296 (tpp) cc_final: 0.2817 (mmp) outliers start: 21 outliers final: 14 residues processed: 170 average time/residue: 2.5986 time to fit residues: 499.2883 Evaluate side-chains 166 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15920 Z= 0.252 Angle : 0.493 7.666 21480 Z= 0.261 Chirality : 0.034 0.128 2316 Planarity : 0.004 0.046 2708 Dihedral : 6.042 60.587 2132 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.61 % Allowed : 25.50 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 1868 helix: 1.87 (0.14), residues: 1468 sheet: None (None), residues: 0 loop : -0.04 (0.37), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 344 HIS 0.001 0.000 HIS B 96 PHE 0.014 0.001 PHE G 304 TYR 0.012 0.001 TYR B 571 ARG 0.002 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6243 (m) cc_final: 0.5720 (t) REVERT: A 198 ARG cc_start: 0.4880 (mtt180) cc_final: 0.4637 (tpt-90) REVERT: A 322 GLU cc_start: 0.7479 (pp20) cc_final: 0.7242 (pp20) REVERT: A 344 TRP cc_start: 0.3583 (t-100) cc_final: 0.3190 (t-100) REVERT: B 161 LEU cc_start: 0.8248 (tt) cc_final: 0.7895 (tm) REVERT: B 214 ARG cc_start: 0.8611 (tpp80) cc_final: 0.7982 (mtp85) REVERT: B 578 MET cc_start: 0.2899 (ttt) cc_final: 0.2633 (ttt) REVERT: C 110 MET cc_start: 0.3996 (tpp) cc_final: 0.2954 (mmp) REVERT: D 80 PHE cc_start: 0.8461 (t80) cc_final: 0.8260 (t80) REVERT: D 214 ARG cc_start: 0.8413 (tpp80) cc_final: 0.7838 (mtt90) REVERT: E 110 MET cc_start: 0.4307 (tpp) cc_final: 0.3148 (mmp) REVERT: F 110 MET cc_start: 0.4039 (tpp) cc_final: 0.2621 (mmp) REVERT: G 198 ARG cc_start: 0.5302 (mtt180) cc_final: 0.5007 (tpt-90) REVERT: G 289 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7887 (m-40) REVERT: H 110 MET cc_start: 0.4320 (tpp) cc_final: 0.2881 (mmp) outliers start: 26 outliers final: 20 residues processed: 177 average time/residue: 2.4848 time to fit residues: 495.1212 Evaluate side-chains 174 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 30.0000 chunk 158 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 40.0000 chunk 132 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 178 optimal weight: 40.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15920 Z= 0.324 Angle : 0.526 9.259 21480 Z= 0.275 Chirality : 0.035 0.129 2316 Planarity : 0.004 0.047 2708 Dihedral : 6.157 60.589 2132 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.86 % Allowed : 25.25 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.20), residues: 1868 helix: 1.84 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.05 (0.37), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 344 HIS 0.002 0.000 HIS B 96 PHE 0.015 0.001 PHE G 304 TYR 0.015 0.001 TYR A 571 ARG 0.002 0.000 ARG D 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6392 (m) cc_final: 0.5812 (t) REVERT: A 198 ARG cc_start: 0.4920 (mtt180) cc_final: 0.4652 (tpt-90) REVERT: A 322 GLU cc_start: 0.7513 (pp20) cc_final: 0.7285 (pp20) REVERT: A 344 TRP cc_start: 0.3587 (t-100) cc_final: 0.3220 (t-100) REVERT: B 214 ARG cc_start: 0.8619 (tpp80) cc_final: 0.7994 (mtp85) REVERT: B 578 MET cc_start: 0.2901 (ttt) cc_final: 0.2640 (ttt) REVERT: C 110 MET cc_start: 0.4031 (tpp) cc_final: 0.3001 (mmp) REVERT: D 214 ARG cc_start: 0.8419 (tpp80) cc_final: 0.7854 (mtt90) REVERT: E 110 MET cc_start: 0.4308 (tpp) cc_final: 0.3177 (mmp) REVERT: F 110 MET cc_start: 0.4048 (tpp) cc_final: 0.2647 (mmp) REVERT: G 198 ARG cc_start: 0.5322 (mtt180) cc_final: 0.5022 (tpt-90) REVERT: G 214 ARG cc_start: 0.8365 (tpp80) cc_final: 0.7748 (mtt90) REVERT: G 289 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7961 (m-40) REVERT: H 110 MET cc_start: 0.4331 (tpp) cc_final: 0.2911 (mmp) outliers start: 30 outliers final: 23 residues processed: 180 average time/residue: 2.5488 time to fit residues: 515.8192 Evaluate side-chains 181 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 115 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 158 optimal weight: 0.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15920 Z= 0.367 Angle : 0.541 9.946 21480 Z= 0.286 Chirality : 0.036 0.136 2316 Planarity : 0.004 0.048 2708 Dihedral : 6.091 59.881 2132 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.55 % Allowed : 25.50 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.20), residues: 1868 helix: 1.78 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -0.05 (0.37), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 344 HIS 0.002 0.001 HIS A 96 PHE 0.016 0.001 PHE B 304 TYR 0.015 0.001 TYR G 571 ARG 0.002 0.000 ARG D 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3736 Ramachandran restraints generated. 1868 Oldfield, 0 Emsley, 1868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 CYS cc_start: 0.6356 (m) cc_final: 0.5671 (t) REVERT: A 198 ARG cc_start: 0.4913 (mtt180) cc_final: 0.4659 (tpt-90) REVERT: A 322 GLU cc_start: 0.7503 (pp20) cc_final: 0.7288 (pp20) REVERT: A 344 TRP cc_start: 0.3613 (t-100) cc_final: 0.3230 (t-100) REVERT: B 214 ARG cc_start: 0.8622 (tpp80) cc_final: 0.7999 (mtp85) REVERT: B 289 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.7799 (m-40) REVERT: B 578 MET cc_start: 0.3178 (ttt) cc_final: 0.2903 (ttt) REVERT: C 110 MET cc_start: 0.4055 (tpp) cc_final: 0.3048 (mmp) REVERT: D 214 ARG cc_start: 0.8431 (tpp80) cc_final: 0.7863 (mtt90) REVERT: E 110 MET cc_start: 0.4255 (tpp) cc_final: 0.3080 (mmp) REVERT: F 110 MET cc_start: 0.4204 (tpp) cc_final: 0.2829 (mmp) REVERT: G 198 ARG cc_start: 0.5310 (mtt180) cc_final: 0.5024 (tpt-90) REVERT: G 289 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8029 (m110) REVERT: H 110 MET cc_start: 0.4335 (tpp) cc_final: 0.2872 (mmp) outliers start: 25 outliers final: 21 residues processed: 174 average time/residue: 2.5337 time to fit residues: 498.7006 Evaluate side-chains 177 residues out of total 1616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain G residue 358 SER Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.247072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129045 restraints weight = 52641.273| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.21 r_work: 0.3244 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2477 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: